geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response

Researchers must be able to generate experimentally testable hypotheses from sequencing-based observational microbiome experiments to discover the mechanisms underlying the influence of gut microbes on human health. We describe geneshot, a novel bioinformatics tool for identifying testable hypothese...

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Autores principales: Minot, Samuel S., Barry, Kevin C., Kasman, Caroline, Golob, Jonathan L., Willis, Amy D.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2021
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097837/
https://www.ncbi.nlm.nih.gov/pubmed/33952321
http://dx.doi.org/10.1186/s13059-021-02355-6
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author Minot, Samuel S.
Barry, Kevin C.
Kasman, Caroline
Golob, Jonathan L.
Willis, Amy D.
author_facet Minot, Samuel S.
Barry, Kevin C.
Kasman, Caroline
Golob, Jonathan L.
Willis, Amy D.
author_sort Minot, Samuel S.
collection PubMed
description Researchers must be able to generate experimentally testable hypotheses from sequencing-based observational microbiome experiments to discover the mechanisms underlying the influence of gut microbes on human health. We describe geneshot, a novel bioinformatics tool for identifying testable hypotheses based on gene-level metagenomic analysis of WGS microbiome data. By applying geneshot to two independent previously published cohorts, we identify microbial genomic islands consistently associated with response to immune checkpoint inhibitor (ICI)-based cancer treatment in culturable type strains. The identified genomic islands are within operons involved in type II secretion, TonB-dependent transport, and bacteriophage growth. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02355-6.
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spelling pubmed-80978372021-05-05 geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response Minot, Samuel S. Barry, Kevin C. Kasman, Caroline Golob, Jonathan L. Willis, Amy D. Genome Biol Method Researchers must be able to generate experimentally testable hypotheses from sequencing-based observational microbiome experiments to discover the mechanisms underlying the influence of gut microbes on human health. We describe geneshot, a novel bioinformatics tool for identifying testable hypotheses based on gene-level metagenomic analysis of WGS microbiome data. By applying geneshot to two independent previously published cohorts, we identify microbial genomic islands consistently associated with response to immune checkpoint inhibitor (ICI)-based cancer treatment in culturable type strains. The identified genomic islands are within operons involved in type II secretion, TonB-dependent transport, and bacteriophage growth. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s13059-021-02355-6. BioMed Central 2021-05-05 /pmc/articles/PMC8097837/ /pubmed/33952321 http://dx.doi.org/10.1186/s13059-021-02355-6 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/ (https://creativecommons.org/publicdomain/zero/1.0/) ) applies to the data made available in this article, unless otherwise stated in a credit line to the data.
spellingShingle Method
Minot, Samuel S.
Barry, Kevin C.
Kasman, Caroline
Golob, Jonathan L.
Willis, Amy D.
geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response
title geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response
title_full geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response
title_fullStr geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response
title_full_unstemmed geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response
title_short geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response
title_sort geneshot: gene-level metagenomics identifies genome islands associated with immunotherapy response
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8097837/
https://www.ncbi.nlm.nih.gov/pubmed/33952321
http://dx.doi.org/10.1186/s13059-021-02355-6
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